Stress and recovery, natural variation, gene expression and QTL

L.B. Snoek, K. Jovic, M.G. Sterken, J.E. Kammenga

Research output: Contribution to conferenceAbstractAcademic

Abstract

C. elegans serves as an important model for integrative analysis of stress
response. Analyzing the transcriptional regulation of stress response and
subsequent recovery provides insight into the mechanisms of fitness
optimization. Although C. elegans stress responses are well studied, the
recovery from stress is poorly understood. We investigated the
transcriptional response over the course of a heat-shock experiment in fully
sequenced recombinant inbred lines (RILs). This allowed us to identify
regulatory loci for stress recovery.
The RILs, derived from a cross between N2 and CB4856, were exposed to
heat-shock after which they were allowed to recover. In both environments,
and in a control environment (no heat stress), genome-wide expression
levels were measured. We then performed expression quantitative trait loci
(eQTL) mapping across these three environments to identify regulatory loci
that contribute to the recovery response.
Across all RILs the largest difference in gene expression was found
between control and heat-shock. Recovering populations showed patterns of
gene expression that were in-between the control and heat-shock. Some
RILs had a more control-like gene expression phenotype while other RILs
were more heat-shock-like, thus allowing for mapping of loci regulating
genetic variation in recovery. We found that genetic variation in gene
expression was largely independent of the environment. More specifically,
approximately 50% of the eQTL were similar in location and effect over the
three environments; therefore did not display interaction with the
environment. Only 1% of the genes with an eQTL in all environments
displayed environment-specific interaction. The remainder of the eQTL
with an environment-specific interaction were specifically detected in one
environment.
In conclusion, the combination of natural variation and gene expression
over the course of a stress response allows for mapping loci underlying
regulation in this response. The genes with an eQTL displaying
environment interaction are specific for one environment. Incorporation of
environment interactions facilitates specifying groups of related eQTL and
thereby allows for detailed eQTL network analysis.
Original languageEnglish
Publication statusPublished - 2016
EventEvolutionary Biology of Caenorhabditis and other nematodes - Cold Spring Harbor Laboratory, Cold Spring Harbor, United States
Duration: 30 Mar 20162 Apr 2016

Conference

ConferenceEvolutionary Biology of Caenorhabditis and other nematodes
CountryUnited States
CityCold Spring Harbor
Period30/03/162/04/16

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quantitative trait loci
heat stress
gene expression
inbred lines
stress response
loci
genes
phenotype
genetic variation
genome

Cite this

Snoek, L. B., Jovic, K., Sterken, M. G., & Kammenga, J. E. (2016). Stress and recovery, natural variation, gene expression and QTL. Abstract from Evolutionary Biology of Caenorhabditis and other nematodes, Cold Spring Harbor, United States.
Snoek, L.B. ; Jovic, K. ; Sterken, M.G. ; Kammenga, J.E. / Stress and recovery, natural variation, gene expression and QTL. Abstract from Evolutionary Biology of Caenorhabditis and other nematodes, Cold Spring Harbor, United States.
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abstract = "C. elegans serves as an important model for integrative analysis of stressresponse. Analyzing the transcriptional regulation of stress response andsubsequent recovery provides insight into the mechanisms of fitnessoptimization. Although C. elegans stress responses are well studied, therecovery from stress is poorly understood. We investigated thetranscriptional response over the course of a heat-shock experiment in fullysequenced recombinant inbred lines (RILs). This allowed us to identifyregulatory loci for stress recovery.The RILs, derived from a cross between N2 and CB4856, were exposed toheat-shock after which they were allowed to recover. In both environments,and in a control environment (no heat stress), genome-wide expressionlevels were measured. We then performed expression quantitative trait loci(eQTL) mapping across these three environments to identify regulatory locithat contribute to the recovery response.Across all RILs the largest difference in gene expression was foundbetween control and heat-shock. Recovering populations showed patterns ofgene expression that were in-between the control and heat-shock. SomeRILs had a more control-like gene expression phenotype while other RILswere more heat-shock-like, thus allowing for mapping of loci regulatinggenetic variation in recovery. We found that genetic variation in geneexpression was largely independent of the environment. More specifically,approximately 50{\%} of the eQTL were similar in location and effect over thethree environments; therefore did not display interaction with theenvironment. Only 1{\%} of the genes with an eQTL in all environmentsdisplayed environment-specific interaction. The remainder of the eQTLwith an environment-specific interaction were specifically detected in oneenvironment.In conclusion, the combination of natural variation and gene expressionover the course of a stress response allows for mapping loci underlyingregulation in this response. The genes with an eQTL displayingenvironment interaction are specific for one environment. Incorporation ofenvironment interactions facilitates specifying groups of related eQTL andthereby allows for detailed eQTL network analysis.",
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Snoek, LB, Jovic, K, Sterken, MG & Kammenga, JE 2016, 'Stress and recovery, natural variation, gene expression and QTL', Cold Spring Harbor, United States, 30/03/16 - 2/04/16, .

Stress and recovery, natural variation, gene expression and QTL. / Snoek, L.B.; Jovic, K.; Sterken, M.G.; Kammenga, J.E.

2016. Abstract from Evolutionary Biology of Caenorhabditis and other nematodes, Cold Spring Harbor, United States.

Research output: Contribution to conferenceAbstractAcademic

TY - CONF

T1 - Stress and recovery, natural variation, gene expression and QTL

AU - Snoek, L.B.

AU - Jovic, K.

AU - Sterken, M.G.

AU - Kammenga, J.E.

PY - 2016

Y1 - 2016

N2 - C. elegans serves as an important model for integrative analysis of stressresponse. Analyzing the transcriptional regulation of stress response andsubsequent recovery provides insight into the mechanisms of fitnessoptimization. Although C. elegans stress responses are well studied, therecovery from stress is poorly understood. We investigated thetranscriptional response over the course of a heat-shock experiment in fullysequenced recombinant inbred lines (RILs). This allowed us to identifyregulatory loci for stress recovery.The RILs, derived from a cross between N2 and CB4856, were exposed toheat-shock after which they were allowed to recover. In both environments,and in a control environment (no heat stress), genome-wide expressionlevels were measured. We then performed expression quantitative trait loci(eQTL) mapping across these three environments to identify regulatory locithat contribute to the recovery response.Across all RILs the largest difference in gene expression was foundbetween control and heat-shock. Recovering populations showed patterns ofgene expression that were in-between the control and heat-shock. SomeRILs had a more control-like gene expression phenotype while other RILswere more heat-shock-like, thus allowing for mapping of loci regulatinggenetic variation in recovery. We found that genetic variation in geneexpression was largely independent of the environment. More specifically,approximately 50% of the eQTL were similar in location and effect over thethree environments; therefore did not display interaction with theenvironment. Only 1% of the genes with an eQTL in all environmentsdisplayed environment-specific interaction. The remainder of the eQTLwith an environment-specific interaction were specifically detected in oneenvironment.In conclusion, the combination of natural variation and gene expressionover the course of a stress response allows for mapping loci underlyingregulation in this response. The genes with an eQTL displayingenvironment interaction are specific for one environment. Incorporation ofenvironment interactions facilitates specifying groups of related eQTL andthereby allows for detailed eQTL network analysis.

AB - C. elegans serves as an important model for integrative analysis of stressresponse. Analyzing the transcriptional regulation of stress response andsubsequent recovery provides insight into the mechanisms of fitnessoptimization. Although C. elegans stress responses are well studied, therecovery from stress is poorly understood. We investigated thetranscriptional response over the course of a heat-shock experiment in fullysequenced recombinant inbred lines (RILs). This allowed us to identifyregulatory loci for stress recovery.The RILs, derived from a cross between N2 and CB4856, were exposed toheat-shock after which they were allowed to recover. In both environments,and in a control environment (no heat stress), genome-wide expressionlevels were measured. We then performed expression quantitative trait loci(eQTL) mapping across these three environments to identify regulatory locithat contribute to the recovery response.Across all RILs the largest difference in gene expression was foundbetween control and heat-shock. Recovering populations showed patterns ofgene expression that were in-between the control and heat-shock. SomeRILs had a more control-like gene expression phenotype while other RILswere more heat-shock-like, thus allowing for mapping of loci regulatinggenetic variation in recovery. We found that genetic variation in geneexpression was largely independent of the environment. More specifically,approximately 50% of the eQTL were similar in location and effect over thethree environments; therefore did not display interaction with theenvironment. Only 1% of the genes with an eQTL in all environmentsdisplayed environment-specific interaction. The remainder of the eQTLwith an environment-specific interaction were specifically detected in oneenvironment.In conclusion, the combination of natural variation and gene expressionover the course of a stress response allows for mapping loci underlyingregulation in this response. The genes with an eQTL displayingenvironment interaction are specific for one environment. Incorporation ofenvironment interactions facilitates specifying groups of related eQTL andthereby allows for detailed eQTL network analysis.

M3 - Abstract

ER -

Snoek LB, Jovic K, Sterken MG, Kammenga JE. Stress and recovery, natural variation, gene expression and QTL. 2016. Abstract from Evolutionary Biology of Caenorhabditis and other nematodes, Cold Spring Harbor, United States.